See mailing list. The spec. should be clear on how the regions are becoming the containing block of the flow element fragments.
For example:
<div style="flow-into:article;width:50%">...</div>
flowing in regionA and regionB with different sizes.
The width of the div will be 50% of the regionA width for the fragment that flows in regionA and 50% of the regionB width for the fragment that flows in regionB.